MolNFT v1 · #61650 · protein
HIV reverse transcriptase K103N mutant in complex with inhibitor R8D
3DRS · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “HIV reverse transcriptase K103N mutant in complex with inhibitor R8D”. X-ray diffraction, 1 ligand (R8D), 13 pockets (best druggability 0.74). MolNFT v1 #61650 on GenesisL1: 3D structure…
- PDB
- 3DRS
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P66 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P04585
- Ligands
- R8D
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 549 | 31% helix, 22% strand | P04585 |
| B | P66 rt | protein | 405 | 38% helix, 20% strand | P04585 |
Ligands and binding sites
- R8D · 3-chloro-5-[2-chloro-5-(1H-pyrazolo[3,4-b]pyridin-3-ylmethoxy)phenoxy]benzonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.74 | 0.80 | 59 | empty |
| 2 | 851 | 0.74 | 0.78 | 78 | empty |
| 3 | 252 | 0.72 | 0.86 | 43 | R8D |
| 4 | 321 | 0.69 | 0.83 | 38 | empty |
| 5 | 292 | 0.57 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2633 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3DRS · HIV reverse transcriptase K103N mutant in complex with inhibitor R8D · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P04585
- Elsewhere: RCSB PDB 3DRS · PDBe 3DRS · UniProt P04585
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